The role of ancient and recent reticulate evolution as a major driver of Narcissus diversity

Reticulation is a key mechanism in plant evolution, impacting diversification, speciation, and distributional patterns. This leads to complex evolutionary relationships that are challenging to classify taxonomically. Discrepancies between both morphological classifications and between molecular phylogenies of Narcissus have led to contested evolutionary relationships and taxonomic treatments. This has been attributed to extensive hybridisation and polyploidy across the genus, which plastid DNA data alone has not been sufficient to resolve. Using whole plastome genomes alongside 261 low-copy nuclear genes, we assess cytonuclear discordance using phylogenetic network techniques to determine the extent of incongruence attributable to hybridisation and introgression events across the genus. Whilst Narcissus and both subgenera are recovered as monophyletic, congruent with morphology-based classifications, several sections were recovered as para- or polyphyletic in both our nuclear and plastome phylogenies. The high levels of cytonuclear discordance recovered and incongruence with morphological classifications were attributed to multiple ancient hybridisation events, including the origin of subsection Narcissus, five sections, and two species, of which we suggest they should be treated at the same rank as their parental lineages. The inclusion of 261 low-copy nuclear genes and use of phylogenetic network methods has elucidated the significance of ancient hybridisation events in the evolutionary history of Narcissus. Accounting for reticulate evolution, particularly of major lineages, is essential when conducting taxonomic revisions of the genus.